US7387875B2 - Methods for monitoring multiple gene expression - Google Patents

Methods for monitoring multiple gene expression Download PDF

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US7387875B2
US7387875B2 US10/950,009 US95000904A US7387875B2 US 7387875 B2 US7387875 B2 US 7387875B2 US 95000904 A US95000904 A US 95000904A US 7387875 B2 US7387875 B2 US 7387875B2
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hypothetical protein
gibberella zeae
filamentous fungal
array
fungal cells
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Randy Berka
Elena Bachkirova
Michael Rey
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Novozymes Inc
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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/158—Expression markers

Definitions

  • the present invention relates to methods for monitoring expression of a plurality of genes in filamentous fungal cells.
  • the present invention also relates to substrates and computer readable media for monitoring expression of a plurality of genes in filamentous fungal cells.
  • Microarray technology is increasingly becoming the method of choice for the quantitative and simultaneous analysis of the expression levels of many thousands of genes.
  • Microarray analyses typically follow the steps of gene selection, microarray synthesis, sample preparation, array hybridization, detection, and data analysis (Watson et al., 1998 , Current Opinion in Biotechnology 9: 609-614).
  • PCR-amplified coding sequences of genomic DNA are particularly useful in microarrays for obtaining global expression profiles where the genome of the organism has been fully sequenced.
  • Chu et al., 1998 , Science 282: 699-705 disclose the use of microarrays containing PCR-amplified genomic coding sequences for determining the temporal expression of Saccharomyces cerevisiae genes during sporulation.
  • global expression profiles may be obtained with arraying (1) random genomic DNA segments or clones (e.g., from a genomic DNA library); (2) random cDNA clones (e.g., from one or more cDNA libraries) that are uncharacterized at the DNA sequence level; (3) EST clones that have been sequenced and partially characterized with respect to putative identification and function; or (4) cDNA clones that are enriched for differentially expressed sequences (Diatchenko et al., 1996 , Proc Natl. Acad. Sci. USA 93: 6025-6030).
  • Expressed sequenced tags are partial cDNA sequences of expressed genes. Simply stated, an EST is a segment of a sequence from a cDNA clone that corresponds to the mRNA of a specific gene.
  • sequenced ESTs in microarrays compared to genomic clones or random cDNA clones provides several advantages especially for organisms whose genomes have not been sequenced. First, redundancy is eliminated because one spot on an array equals one gene or open reading frame. Second, since sequence information is available, redundancy and follow-up characterization is minimized. Third, EST microarrays can be organized based on function of the gene products to facilitate analysis of the results (e.g., ESTs encoding enzymes from the same metabolic pathway can be arranged or grouped accordingly).
  • SSH suppression subtractive hybridization
  • WO 2000/56762 discloses methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells using microarrays containing filamentous fungal expressed sequenced tags.
  • Filamentous fungi are increasingly being used as host microorganisms for the industrial production of enzymes and other proteins whether endogenous or heterogenous to the microorganisms.
  • the present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells, comprising:
  • nucleic acids from the first filamentous fungal cell and the one or more second filamentous fungal cells are labeled with a first detection reporter and one or more different second detection reporters, respectively;
  • the present invention also relates to computer readable media and substrates containing an array of such Trichoderma reesei ESTs or SSH clones, or a combination thereof, for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells.
  • FIG. 1 show the SSH method for generation of subtractive and normalized cDNA libraries.
  • the present invention relates to methods for monitoring differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells.
  • the methods comprise (a) adding a mixture of detection reporter-labeled nucleic acids isolated from the two or more filamentous fungal cells with different detection reporters for each cell's nucleic acids to a substrate containing an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof, under conditions where the nucleic acids hybridize to complementary sequences of the ESTs or SSH clones, or a combination thereof, in the array; and (b) examining the array under conditions wherein the relative expression of the genes in the two or more cells is determined by the observed detection signal of each spot in the array.
  • the methods of the present invention may be used to monitor global expression of a plurality of genes from a filamentous fungal cell, discover new genes, identify possible functions of unknown open reading frames, and monitor gene copy number variation and stability.
  • the global view of changes in expression of genes may be used to provide a picture of the way in which filamentous fungal cells adapt to changes in culture conditions, environmental stress, or other physiological provocation.
  • Other possibilities for monitoring global expression include spore morphogenesis, recombination, metabolic or catabolic pathway engineering.
  • the methods of the present invention are used to identify microbial genes induced when the microorganism is grown on cellulose or corn stover.
  • the microorganism is a Trichoderma strain.
  • the microorganism is a Trichoderma reesei strain.
  • the methods of the present invention are particularly advantageous because one spot on an array equals one gene or open reading frame, extensive follow-up characterization is unnecessary since sequence information is available, and EST and/or SSH microarrays can be organized based on function of the gene products.
  • array features is defined herein as array elements of ESTs or SSH clones, or a combination thereof.
  • EST expressed sequenced tag
  • EST is defined herein as a segment of a sequence from a cDNA clone of an expressed Trichoderma reesei gene.
  • EST will be understood to also include two or more ESTs assembled into a contig.
  • the Trichoderma reesei ESTs described herein preferably represent a plurality of genes or homologues thereof present in the two or more filamentous fungal cells to be evaluated.
  • ESTs are generally generated as follows: Total polyadenylated mRNA is isolated from a filamentous fungal cell and reverse transcribed into total cDNA. The total cDNA is digested with a restriction endonuclease, size-selected by agarose gel electrophoresis, isolated, and ligated into a vector, e.g., pZErO-2.1. The ligation mixture is transformed into competent E. coli cells and transformants are selected under selective pressure, e.g., kanamycin selection. The cDNA clones isolated from the selected transformants are amplified, isolated, and partially sequenced. The partial sequences are then compared to sequences in various publicly available databases for identification.
  • Any method known in the art may be used for generating ESTs (see, for example, Adams et al., 1991 , Science 252: 1651-1656; Fields, 1996 , Tibtech 14: 286-289; Weinstock et al., 1994 , Current Opinion in Biotechnology 5: 599-603; Matsubara and Okubo, 1993 , Current Opinions in Biotechnology 4: 672-677; Nelson et al., 1997 , Fungal Genet. Biol. 21: 348-363; Zhu at al., Genetics 157: 1057-1065).
  • the ESTs are SEQ ID NOs: 1-24.
  • SSH clones is defined herein as selectively amplified target cDNA fragments which are differentially expressed. SSH is used to selectively amplify these target cDNA fragments and simultaneously suppress nontarget DNA amplification.
  • the SSH clones are SEQ ID NOs: 25-65.
  • the Trichoderma reesei array features are preferably at least about 50 bp in length, more preferably at least about 100 bp in length, even more preferably at least about 150 bp in length, and most preferably at least about 200 bp in length.
  • the array features are preferably directional ESTs or SSH clones, or a combination thereof.
  • nondirectional ESTs or SSH clones, or a combination thereof may also be used.
  • a “directional EST” is defined as a cDNA cloned in the same orientation relative to the vector cloning sites, e.g., 5′ ⁇ 3′ or 3′ ⁇ 5′.
  • the array features are obtained from Trichoderma reesei .
  • the array features are obtained from Trichoderma reesei strain RutC30 (Montenecourt and Eveleigh, 1979 , Adv. Chem. Ser. 181: 289-301).
  • the Trichoderma reesei array features are selected from the group consisting of SEQ ID NOs. 1-1188, nucleic acid fragments of SEQ ID NOs. 1-1188, or nucleic acid sequences having at least 95%, preferably at least 99% and most preferably at least 99.9% homology to a sequence of SEQ ID NOs. 1-1188.
  • the array features obtained from Trichoderma reesei are ESTs. In another preferred embodiment, the array features obtained from Trichoderma reesei are SSH clones. In another preferred embodiment, the array features obtained from Trichoderma reesei are a combination of two or more of ESTs and SSH clones.
  • an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof is defined herein as a linear or two-dimensional array of preferably discrete array features, each having a finite area, formed on the surface of a solid support.
  • microarray is defined herein as an array of features (i.e., ESTs or SSH clones, or a combination thereof) having a density of discrete array elements of at least about 100/cm 2 , and preferably at least about 1000/cm 2 .
  • the printed elements in a microarray have typical dimensions, e.g., diameters, in the range of between about 10 to about 250 ⁇ m, preferably in the range of between about 10 to about 200 ⁇ m, more preferably in the range of between about 20 to about 150 ⁇ m, even more preferably in the range of between about 20 to about 100 ⁇ m, most preferably in the range of between about 20 to about 75 ⁇ m, and even most preferably in the range of between about 25 to about 50 ⁇ m, and are separated from other printed elements in the microarray by about the same distance.
  • a substrate containing an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof is defined herein as a solid support having deposited on the surface of the support one or more of a plurality of array features, for use in detecting binding of labeled cDNAs to the array features.
  • the substrate may, in one aspect, be a glass support (eg., glass slide) having a hydrophilic or hydrophobic coating on the surface of the support, and an array of distinct array features electrostatically bound non-covalently to the coating, where each distinct array features is disposed at a separate, defined position.
  • a glass support eg., glass slide
  • an array of distinct array features electrostatically bound non-covalently to the coating, where each distinct array features is disposed at a separate, defined position.
  • Each microarray in the substrate preferably contains at least 10 3 distinct array features in a surface area of less than about 1 cm 2 .
  • Each distinct array feature (i) is disposed at a separate, defined position in the array, (ii) has a length of at least 50 bp, and (iii) is present in a defined amount between about 0.1 femtomoles and 100 nanomoles or higher if necessary.
  • the glass slide is coated by placing a film of a polycationic polymer with a uniform thickness on the surface of the slide and drying the film to form a dried coating.
  • the amount of polycationic polymer added should be sufficient to form at least a monolayer of polymers on the glass surface.
  • the polymer film is bound to the surface via electrostatic binding between negative silyl-OH groups on the surface and charged cationic groups in the polymers.
  • Such polycationic polymers include, but are not limited to, polylysine and polyarginine.
  • Another coating strategy employs reactive aldehydes to couple DNA to the slides (Schena et al., 1996 , Proceedings of the National Academy of Science USA 93: 10614-10619; Heller at al., 1997 , Proceedings of the National Academy of Science USA 94: 2150-2155).
  • the surface may have a relatively hydrophobic character, i.e., one that causes aqueous medium deposited on the surface to bead.
  • a relatively hydrophobic character i.e., one that causes aqueous medium deposited on the surface to bead.
  • hydrophobic polymers such as polystyrene, polypropylene, or polyethylene, have desirable hydrophobic properties, as do glass and a variety of lubricant or other hydrophobic films that may be applied to the support surface.
  • a support surface is “hydrophobic” if an aqueous droplet applied to the surface does not spread out substantially beyond the area size of the applied droplet, wherein the surface acts to prevent spreading of the droplet applied to the surface by hydrophobic interaction with the droplet.
  • the substrate may be a multi-cell substrate where each cell contains a microarray of array features, and preferably an identical microarray, formed on a porous surface.
  • a 96-cell array may typically have array dimensions between about 12 and 244 mm in width and 8 and 400 mm in length, with the cells in the array having width and length dimension of 1/12 and 1 ⁇ 8 the array width and length dimensions, respectively, i.e., between about 1 and 20 in width and 1 and 50 mm in length.
  • the solid support may include a water-impermeable backing such as a glass slide or rigid polymer sheet, or other non-porous material.
  • a water-permeable film which is made of porous material.
  • porous materials include, but are not limited to, nitrocellulose membrane nylon, polypropylene, and PVDF polymer.
  • the thickness of the film is preferably between about 10 and 1000 ⁇ m.
  • the film may be applied to the backing by spraying or coating, or by applying a preformed membrane to the backing.
  • the film surface may be partitioned into a desirable array of cells by water-impermeable grid lines typically at a distance of about 100 to 2000 ⁇ m above the film surface.
  • the grid lines can be formed on the surface of the film by laying down an uncured flowable resin or elastomer solution in an array grid, allowing the material to infiltrate the porous film down to the backing, and then curing the grid lines to form the cell-array substrate.
  • the barrier material of the grid lines may be a flowable silicone, wax-based material, thermoset material (e.g., epoxy), or any other useful material.
  • the grid lines may be applied to the solid support using a narrow syringe, printing techniques, heat-seal stamping, or any other useful method known in the art.
  • Each well preferably contains a microarray of distinct array features.
  • “Distinct array features” as applied to the ESTs or SSH clones, or a combination thereof, forming a microarray is defined herein as an array feature which is distinct from other array features on the basis of a different nucleic add sequence, and/or different concentrations of the same or distinct array features, and/or different mixtures of distinct array features or different-concentrations of array features.
  • an array of “distinct array features” may be an array containing, as its components, (i) distinct array features, which may have a defined amount in each component, (ii) different, graded concentrations of given-sequence array features, and/or (iii) different-composition mixtures of two or more distinct array features.
  • the delivery of a known amount of a selected EST or SSH clone to a specific position on the support surface is preferably performed with a dispensing device equipped with one or more tips for insuring reproducible deposition and location of the array features and for preparing multiple arrays.
  • a dispensing device equipped with one or more tips for insuring reproducible deposition and location of the array features and for preparing multiple arrays.
  • Any dispensing device known in the art may be used in the methods of the present invention. See, for example, U.S. Pat. No. 5,807,522.
  • the dispensing device preferably contains a plurality of tips.
  • the liquid will have less of a tendency to bead, and the dispensed volume will be more sensitive to the total dwell time of the dispenser tip in the immediate vicinity of the support surface.
  • flow of fluid from the tip onto the support surface will continue from the dispenser onto the support surface until it forms a liquid bead.
  • a given bead size i.e., volume
  • the tendency of liquid to flow onto the surface will be balanced by the hydrophobic surface interaction of the bead with the support surface, which acts to limit the total bead area on the surface, and by the surface tension of the droplet, which tends toward a given bead curvature.
  • a given bead volume will have formed, and continued contact of the dispenser tip with the bead, as the dispenser tip is being withdrawn, will have little or no effect on bead volume.
  • the desired deposition volume, i.e., bead volume, formed is preferably in the range 2 ⁇ l (picoliters) to 2 nl (nanoliters), although volumes as high as 100 nl or more may be dispensed. It will be appreciated that the selected dispensed volume will depend on (i) the “footprint” of the dispenser tip(s), i.e., the size of the area spanned by the tip(s), (ii) the hydrophobicity of the support surface, and (iii) the time of contact with and rate of withdrawal of the tip(s) from the support surface.
  • bead size may be reduced by increasing the viscosity of the medium, effectively reducing the flow time of liquid from the dispensing device onto the support surface.
  • the drop size may be further constrained by depositing the drop in a hydrophilic region surrounded by a hydrophobic grid pattern on the support surface.
  • bead volume can be reduced in a controlled fashion by increasing surface hydrophobicity, reducing time of contact of the tip with the surface, increasing rate of movement of the tip away from the surface, and/or increasing the viscosity of the medium. Once these parameters are fixed, a selected deposition volume in the desired pl to nl range can be achieved in a repeatable fashion.
  • the tip After depositing a liquid droplet of an array feature sample at one selected location on a support, the tip may be moved to a corresponding position on a second support, the sample is deposited at that position, and this process is repeated until the sample has been deposited at a selected position on a plurality of supports.
  • This deposition process may then be repeated with another EST or SSH clone sample at another microarray position on each of the supports.
  • each array feature region is preferably between about 20-200 ⁇ m.
  • the spacing between each region and its closest (non-diagonal) neighbor, measured from center-to-center, is preferably in the range of about 20-400 ⁇ m.
  • an array having a center-to-center spacing of about 250 ⁇ m contains about 40 regions/cm 2 or 1,600 regions/cm 2 .
  • the support is treated to evaporate the liquid of the droplet forming each region, to leave a desired array of dried, relatively flat array feature regions. This drying may be done by heating or under vacuum.
  • the two or more filamentous fungal cells may be any filamentous fungal cell where one of the cells is used as a reference for identifying differences in expression of the same or similar complement of genes in the other cell.
  • the two or more cells are the same cell. For example, they may be compared under different growth conditions, e.g., carbon source, oxygen limitation, nutrition, and/or physiology.
  • one or more cells are mutants of the reference cell. For example, the mutant(s) may have a different phenotype.
  • the two or more cells are of different species (e.g., Trichoderma reesei and Trichoderma viride ).
  • the two or more cells are of different genera.
  • one or more cells are transformants of the reference cell, wherein the one or more transformants exhibit a different property.
  • the transformants may have a different or improved phenotype relative to the reference cell and/or one of the other transformants.
  • phenotype is defined herein as an observable or outward characteristic of a cell determined by its genotype and modulated by its environment.
  • Such different or improved phenotypes may include, but are not limited to, improved secretion or production of a protein or compound, reduced or no secretion or production of a protein or compound, improved or reduced expression of a gene, desirable morphology, an altered growth rate under desired conditions, relief of over-expression mediated growth inhibition, or tolerance to low oxygen conditions, improved filterability or flocculation properties, or altered protein glycosylation.
  • the differential expression of a plurality of genes in a first filamentous fungal cell relative to expression of the same genes in one or more second filamentous fungal cells is a result of growth of the first filamentous fungal cell on glucose and growth of the one or more second filamentous fungal cells on cellulose, hemicellulose, and/or corn stover to identify genes that are induced by growth on cellulose, hemicellulose, or corn stover.
  • the corn stover is preferably pre-treated and washed corn stover as described herein.
  • the filamentous fungal cells may be any filamentous fungal cells, but preferably Acremonium, Aspergillus, Aureobasidium, Bjerkandera, Ceriporiopsis, Coprinus, Coriolus, Cryptococcus, Filibasidium, Fusarium, Humicola, Magnaporthe, Mucor, Myceliophthora, Neocallimastix, Neurospora, Paecilomyces, Penicillium, Phanerochaete, Phlebia, Piromyces, Pleurotus, Schizophyllum, Talaromyces, Thermoascus, Thielavia, Tolypocladium, Trametes , or Trichoderma cells, and more preferably Aspergillus awamori, Aspergillus fumigatus, Aspergillus foetidus, Aspergillus japonicus, Aspergillus nidulans, Aspergillus niger, Aspergillus ory
  • the filamentous fungal cells are Trichoderma cells.
  • the Trichoderma cells are Trichoderma reesei cells.
  • the Trichoderma cells are Trichoderma reesei strain RutC30 (Montenecourt and Eveleigh, 1979, supra).
  • the cells are cultivated in a nutrient medium suitable for growth using methods well known in the art for isolation of the nucleic acids to be used as probes.
  • the cells may be cultivated by shake flask cultivation, small-scale or large-scale fermentation (including continuous, batch, fed-batch, or solid state fermentations) in laboratory or industrial fermentors performed in a suitable medium.
  • the cultivation takes place in a suitable nutrient medium comprising carbon and nitrogen sources and inorganic salts, using procedures known in the art.
  • suitable media are available from commercial suppliers or may be prepared according to published compositions (eg., in catalogues of the American Type Culture Collection).
  • the nucleic acid probes from the two or more filamentous fungal cells may be any nucleic acid including genomic DNA, cDNA, and RNA, and may be isolated using standard methods known in the art.
  • cDNA probes may be obtained from the total polyadenylated mRNA isolated from the cells using standard methods and reverse transcribed into total cDNA.
  • the populations of isolated nucleic acid probes may be labeled with detection reporters such as colorimetric, radioactive, fluorescent reporters, or other reporters using methods known in the art (Chen et al., 1998 , Genomics 51: 313-324; DeRisi et al., 1997 , Science 278: 680-686; U.S. Pat. No. 5,770,367).
  • detection reporters such as colorimetric, radioactive, fluorescent reporters, or other reporters using methods known in the art (Chen et al., 1998 , Genomics 51: 313-324; DeRisi et al., 1997 , Science 278: 680-686; U.S. Pat. No. 5,770,367).
  • the probes are labeled with fluorescent reporters.
  • cDNA probes may be labeled during reverse transcription from the respective mRNA pools by incorporation of fluorophores as dye-labeled nucleotides (DeRisi et al., 1997, supra), e.g., Cy5-labeled deoxyuridine triphosphate, or the isolated cDNAs may be directly labeled with different fluorescent functional groups.
  • Fluorescent-labeled nucleotides include, but are not limited to, fluorescein conjugated nucleotide analogs (green fluorescence) and lissamine nucleotide analogs (red fluorescence).
  • Fluorescent functional groups include, but are not limited to, Cy3 (a green fluorescent dye) and Cy5 (red fluorescent dye).
  • the labeled nucleic acids from the two or more filamentous fungal cells are then added to a substrate containing an array of Trichoderma reesei array features under conditions where the nucleic acid pools from the two or more filamentous fungal cells hybridize to complementary sequences of the array features in the array.
  • hybridization indicates that the labeled nucleic acids from the two or more cells hybridize to the array features under very low to very high stringency conditions.
  • a small volume of the labeled nucleic acids mixture is loaded onto the substrate.
  • the solution will spread to cover the entire microarray.
  • one or more solutions are loaded into each cell which stop at the barrier elements.
  • the labeled probes are denatured and applied to a microarray slide under a cover glass, placed in a humidified chamber, and incubated overnight (15-16 hours) in a water bath at 63° C. Before scanning, the arrays are washed consecutively in 1 ⁇ SSC with 0.03% SDS, 0.2 ⁇ SSC, and 0.05 ⁇ SSC and centrifuged for 2 minutes at 500 rpm top remove excess liquid. For further details, see Berka et al., 2003 , Proc. Natl. Acad. Sci. USA 100: 5682-5687.
  • very low to very high stringency conditions are defined as prehybridization and hybridization at 42° C. in 5 ⁇ SSPE, 0.3% SDS, 200 ⁇ g/ml sheared and denatured salmon sperm DNA, and either 25% formamide for very low and low stringencies, 35% formamide for medium and medium-high stringencies, or 50% formamide for high and very high stringencies, following standard Southern blotting procedures for 12 to 24 hours optimally.
  • the carrier material is finally washed three times each for 15 minutes using 2 ⁇ SSC, 0.2% SDS preferably at least at 45° C. (very low stringency), more preferably at least at 50° C. (low stringency), more preferably at least at 55° C. (medium stringency), more preferably at least at 60° C. (medium-high stringency), even more preferably at least at 65° C. (high stringency), and most preferably at least at 70° C. (very high stringency).
  • stringency conditions are defined as prehybridization, hybridization, and washing post-hybridization at 5° C. to 10° C. below the calculated T m using the calculation according to Bolton and McCarthy (1962 , Proceedings of the National Academy of Sciences USA 48:1390) in 0.9 M NaCl, 0.09 M Tris-HCl pH 7.6, 6 mM EDTA, 0.5% NP-40, 1 ⁇ Denhardt's solution, 1 mM sodium pyrophosphate, 1 mM sodium monobasic phosphate, 0.1 mM ATP, and 0.2 mg of yeast RNA per ml following standard Southern blotting procedures for 12 to 24 hours optimally.
  • the carrier material is washed once in 6 ⁇ SCC plus 0.1% SDS for 15 minutes and twice each for 15 minutes using 6 ⁇ SSC at 5° C. to 10° C. below the calculated T m .
  • hybridization conditions will depend on the degree of homology between the Trichoderma reesei array features and the nucleic acids obtained from the two or more filamentous fungal cells. For example, where the cells are the same cell from which the array features were obtained, high stringency conditions may be most suitable. Where the cells are from a genus or species different from which the Trichoderma reesei array features were obtained, low or medium stringency conditions may be more suitable.
  • the hybridization is conducted under low stringency conditions. In a more preferred embodiment, the hybridization is conducted under medium stringency conditions. In a most preferred embodiment, the hybridization is conducted under high stringency conditions.
  • the entire solid support is then reacted with detection reagents, if needed, and analyzed using standard calorimetric, radioactive, or fluorescent detection means. All processing and detection steps are performed simultaneously to all of the microarrays on the solid support ensuring uniform assay conditions for all of the microarrays on the solid support.
  • the most common detection method is laser-induced fluorescence detection using confocal optics (Cheung et al., 1998 , Nat. Genet. 18: 225-230).
  • the array is examined under fluorescence excitation conditions such that (i) the Trichoderma reesei array features in the array that hybridize to the nucleic acid probes obtained from one of the first cell and one or more second cells produces a distinct first fluorescence emission color or one or second fluorescence emission colors, respectively, and (ii) the Trichoderma reesei ESTs or SSH clones, or a combination thereof, in the array that hybridize to substantially equal numbers of nucleic acid probes obtained from the first cell and one of the one or more second cells produce a distinct combined fluorescence emission color, respectively; wherein the relative expression of the genes in the two or more cells can be determined by the observed fluorescence emission color of each spot in the array.
  • the fluorescence excitation conditions are based on the selection of the fluorescence reporters.
  • Cy3 and Cy5 reporters are detected with solid state lasers operating at 532 nm and 650 nm, respectively.
  • the methods comprise (a) adding a mixture of fluorescence-labeled nucleic acids isolated from the filamentous fungal cells to a substrate containing an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof, selected from the group consisting of SEQ ID NOs. 1-1188, nucleic acid fragments of SEQ ID NOs. 1-1188, and nucleic acid sequences having at least 90% homology to SEQ ID NOs.
  • the data obtained from the scanned image may then be analyzed using any of the commercially available image analysis software.
  • the software preferably identifies array elements, subtracts backgrounds, deconvolutes multi-color images, flags or removes artifacts, verifies that controls have performed properly, and normalizes the signals (Chen et al., 1997 , Journal of Biomedical Optics 2: 364-374).
  • the difference in the detected expression level is at least about 10% or greater, preferably at least about 20% or greater, more preferably at least about 50% or greater, even more preferably at least about 75% or greater; and most preferably at least about 100% or greater.
  • SAM Significance Analysis of Microarrays
  • Cluster algorithms may also be used to analyze microarray expression data. From the analysis of the expression profiles it is possible to identify co-regulated genes that perform common metabolic or biosynthetic functions. Hierarchical clustering has been employed in the analysis of microarray expression data in order to place genes into clusters based on sharing similar patterns of expression (Eisen et al., 1998, supra). This method yields a graphical display that resembles a kind of phylogenetic tree where the relatedness of the expression behavior of each gene to every other gene is depicted by branch lengths. The programs Cluster and TreeView, both written by Michael Eisen (Eisen et al., 1998 Proc. Nat Acad. Sci. USA 95: 14863-14868) are freely available. Genespring is a commercial program available for such analysis (Silicon Genetics, Redwood City, Calif.).
  • SOMs Self-organizing maps
  • This method involves selecting a geometry of nodes, where the number of nodes defines the number of clusters. Then, the number of genes analyzed and the number of experimental conditions that were used to provide the expression values of these genes are subjected to an iterative process (20,000-50,000 iterations) that maps the nodes and data points into multidimensional gene expression space. After the identification of significantly regulated genes, the expression level of each gene is normalized across experiments.
  • the Trichoderma reesei array features described herein may be “provided” in a variety of mediums to facilitate their use.
  • the term “provided” refers to a manufacture comprising an array of Trichoderma array features.
  • Such manufactures provide a large portion of the genomes of Trichoderma reesei and parts thereof (e.g., an open reading frame (ORF)) in a form which allows one skilled in the art to examine the manufacture using means not directly applicable to examining the genome or a subset thereof as it exists in nature or in purified form.
  • ORF open reading frame
  • the present invention also relates to such a manufacture in the form of a computer readable medium comprising an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof.
  • the computer readable medium comprises an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof, selected from the group consisting of SEQ ID NOs. 1-1188, nucleic acid fragments of SEQ ID NOs. 1-1188, or nucleic acid sequences having at least 95%, preferably at least 99% and most preferably at least 99.9% homology to a sequence of SEQ ID NOs. 1-1188.
  • the computer readable medium comprises an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof, selected from the group consisting of SEQ ID NOs. 1-1188.
  • the Trichoderma reesei array features can be recorded on computer readable media.
  • computer readable media is defined herein as any medium which can be read and accessed directly by a computer.
  • Such computer readable media include, but are not limited to, magnetic storage media, e.g., floppy discs, hard disc storage medium, and magnetic tape; optical storage media, e.g., CD-ROM, DVD; electrical storage media, e.g., RAM and ROM; and hybrids of these categories, e.g., magnetic/optical storage media.
  • “recorded” refers to a process for storing information on computer readable medium.
  • One skilled in the art can readily adopt any of the presently known methods for recording information on computer readable medium to generate manufactures comprising the nucleotide sequence information of the present invention.
  • a variety of data storage structures are available for creating a computer readable medium having recorded thereon the Trichoderma reesei array features of the present invention. The choice of the data storage structure will generally be based on the means chosen to access the stored information.
  • a variety of data processor programs and formats can be used to store the nucleotide sequence information of the present invention on computer readable medium.
  • the sequence information can be represented in a word processing text file, formatted in commercially-available software such as WordPerfect and Microsoft Word, or represented in the form of an ASCII file, stored in a database application, such as DB2, Sybase, Oracle, or the like.
  • a skilled artisan can readily adapt any number of data-processor structuring formats (e.g., text file or database) in order to obtain computer readable medium having recorded thereon the nucleotide sequence information of the present invention.
  • ORFs open reading frames
  • the present invention further provides systems, particularly computer-based systems, which contain the sequence information described herein.
  • systems are designed to identify, among other things, genes and gene products—many of which could be products themselves or used to genetically modify an industrial expression host through increased or decreased expression of a specific gene sequence(s).
  • a computer-based system is defined herein as a hardware means, software means, and data storage means used to analyze the nucleotide sequence information of the present invention.
  • the minimum hardware means of the computer-based systems of the present invention comprises a central processing unit (CPU), input means, output means, and data storage means.
  • CPU central processing unit
  • input means input means
  • output means output means
  • data storage means data storage means
  • the computer-based systems of the present invention comprise a data storage means having stored therein nucleic acid sequences of the Trichoderma reesei array features and the necessary hardware means and software means for supporting and implementing a search means.
  • data storage means is defined herein as memory which can store nucleotide sequence information of the present invention, or a memory access means which can access manufactures having recorded thereon the nucleotide sequence information of the present invention.
  • search means is defined herein as one or more programs which are implemented on the computer-based system to compare a target sequence or target structural motif with the sequence information stored within the data storage means. Search means are used to identify fragments or regions of the present sequences which match a particular target sequence or target motif.
  • a variety of known algorithms are disclosed publicly and a variety of commercially available software for conducting search means are and can be used in the computer-based systems of the present invention. Examples of such software includes, but is not limited to, MacPattern (Fuchs, 1991 , Comput Appl. Biosci. 7: 105-106), BLASTN and BLASTX (NCBI).
  • MacPattern Fuchs, 1991 , Comput Appl. Biosci. 7: 105-106
  • BLASTN BLASTN
  • BLASTX NCBI
  • target sequence is defined herein as any DNA or amino acid sequence of six or more nucleotides or two or more amino acids.
  • the most preferred sequence length of a target sequence is from about 10 to 100 amino acids or from about 30 to 300 nucleotide residues.
  • searches for commercially important fragments, such as sequence fragments involved in gene expression and protein processing may be of shorter length.
  • a target structural motif or “target motif” is defined herein as any rationally selected sequence or combination of sequences chosen based on a three-dimensional configuration which is formed upon the folding of the target motif.
  • target motifs include, but are not limited to, enzyme active sites and signal sequences, substrate and cofactor binding domains, transmembrane domains, and sites for post-translational modifications.
  • Nucleic acid target motifs include, but are not limited to, promoter sequences, hairpin structures and inducible expression elements (protein binding sequences), repeats, palindromes, dyad symmetries, intron-exon boundaries, transcription and translation start and stop sites, and polyadenylation signals.
  • a variety of structural formats for the input and output means can be used to input and output the information in the computer-based systems of the present invention.
  • a preferred format for an output means ranks fragments of the nucleic acid sequences possessing varying degrees of homology to the target sequence or target motif. Such presentation provides one skilled in the art with a ranking of sequences which contain various amounts of the target sequence or target motif and identifies the degree of homology contained in the identified fragment.
  • a variety of comparing means can be used to compare a target sequence or target motif with the data storage means to identify sequence fragments of a genome.
  • implementing software which utilize the BLAST and BLAZE algorithms, described in Altschul et al., 1990 , Journal of Molecular Biology 215: 403-410, may be used to identify open reading frames within the Trichoderma reesei genome or the genomes of other organisms.
  • Any one of the publicly available homology search programs can be used as the search means for the computer-based systems of the present invention. Of course, suitable proprietary systems that may be known to those of skill also may be employed in this regard.
  • the present invention also relates to substrates as described herein comprising an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof.
  • the substrate comprises an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof, selected from the group consisting of SEQ ID NOs. 1-1188, nucleic acid fragments of SEQ ID NOs. 1-1188, or nucleic acid sequences having at least 95%, preferably at least 99% and most preferably at least 99.9% homology to a sequence of SEQ ID NOs. 1-1188.
  • the substrate comprises an array of Trichoderma reesei ESTs or SSH clones, or a combination thereof, selected from the group consisting of SEQ ID NOs. 1-1188.
  • Chemicals used as buffers and substrates were commercial products of at least reagent grade.
  • Trichoderma reesei strain RutC30 (Montenecourt and Eveleigh, 1979 , Adv. Chem. Ser. 181: 289-301) was cultivated in a pilot scale fermentation tank in growth medium containing a complex carbon source.
  • the carbon sources included glucose, cellulose, or pre-treated and washed corn stover.
  • Fungal mycelium was collected from a one-liter sample, and immediately frozen in liquid N 2 and stored at ⁇ 80° C.
  • PCS Pretreated corn stover
  • NREL National Renewable Energy Laboratory
  • the water-insoluble solids in PCS include: 56.5% cellulose, 4.6% hemicellulose, and 28.4% lignin.
  • Pretreatment conditions were: corn stover, 1.4% (wt/vol) sulfuric acid, 165° C., 107 psi, for 8 minutes.
  • PCS Prior to assay, PCS was washed with a large volume of distilled deionized water on a glass filter. PCS was then milled using a coffee grinder to reduce particle size, then washed further with water on a 22 ⁇ m Millipore filter (6P Express Membrane, Stericup, Millipore, Billerica, Mass.). The washed PCS was resuspended in deionized water to make a 20 mg/ml suspension, and stored at 4° C.
  • RNA was prepared from the Trichoderma reesei mycelial samples described in Example 1 by extraction with guanidinium thiocyanate followed by ultracentrifugation through a 5.7 M CsCl cushion (Chirgwin et al., 1979 , Biochemistry 18: 5294-5299) using the following modifications.
  • the frozen mycelia were ground in liquid N 2 to a fine powder with a mortar and a pestle, followed by grinding in a precooled coffee mill, and immediately suspended in 5 volumes of RNA extraction buffer (4 M guanidinium thiocyanate, 0.5% sodium laurylsarcosine, 25 mM sodium citrate pH 7.0, 0.1 M ⁇ -mercaptoethanol).
  • the mixture was stirred for 30 minutes at room temperature and centrifuged (20 minutes at 12,000 ⁇ g) to pellet the cell debris.
  • the supernatant was collected, carefully layered onto a 5.7 M CsCl cushion (5.7 M CsCl, 10 mM EDTA, pH 7.5, 0.1% DEPC; autoclaved prior to use) using 26.5 ml supernatant per 12.0 ml of CsCl cushion, and centrifuged to obtain the total RNA (Beckman SW 28 rotor, 25,000 rpm, room temperature, 24 hours). After centrifugation the supernatant was carefully removed and the bottom of the tube containing the RNA pellet was cut off and rinsed with 70% ethanol.
  • RNA pellet was transferred to an Eppendorf tube, suspended in 500 ⁇ l of TE (10 mM Tris-0.1 mM EDTA), pH 7.6 (if difficult, heated occasionally for 5 minutes at 65° C.), phenol extracted, and precipitated with ethanol for 12 hours at ⁇ 20° C. (2.5 volumes of ethanol, 0.1 volume of 3M sodium acetate pH 5.2).
  • TE 10 mM Tris-0.1 mM EDTA
  • pH 7.6 if difficult, heated occasionally for 5 minutes at 65° C.
  • phenol extracted precipitated with ethanol for 12 hours at ⁇ 20° C. (2.5 volumes of ethanol, 0.1 volume of 3M sodium acetate pH 5.2).
  • the RNA was collected by centrifugation (30 minutes at 12,000 ⁇ g), washed in 70% ethanol, and resuspended in a minimum volume of DEPC-treated water.
  • the total RNA concentration was determined by measuring the absorbance at 260 nm.
  • RNA was isolated by oligo(dT)-cellulose affinity chromatography (Aviv & Leder, 1972 , Proceedings of the National Academy of Sciences USA 69: 1408-1412). A total of 0.2 g of oligo(dT) cellulose (Boehringer Mannheim, Indianapolis, Ind.) was pre-swollen in 10 ml of 1 ⁇ of column loading buffer (20 mM Tris-Cl, pH 7.6, 0.5 M NaCl, 1 mM EDTA, 0.1% SDS), loaded onto a DEPC-treated, plugged plastic column (Poly Prep Chromatography Column, BioRad, Hercules, Calif.), and equilibrated with 20 ml of 1 ⁇ loading buffer.
  • column loading buffer (20 mM Tris-Cl, pH 7.6, 0.5 M NaCl, 1 mM EDTA, 0.1% SDS
  • RNA 1-2 mg was heated at 65° C. for 8 minutes, quenched on ice for 5 minutes, and after addition of 1 volume of 2 ⁇ column loading buffer loaded onto the column. The eluate was collected and reloaded 2-3 times by heating the sample as above and quenching on ice prior to each loading.
  • the oligo(dT) column was washed with 10 volumes of 1 ⁇ loading buffer, then with 3 volumes of medium salt buffer (20 mM Tris-Cl, pH 7.6, 0.1 M NaCl, 1 mM EDTA, 0.1% SDS), followed by elution of the poly(A) + RNA with 3 volumes of elution buffer (10 mM Tris-Cl pH 7.6, 1 mM EDTA, 0.05% SDS) preheated to 65° C., by collecting 500 ⁇ l fractions. The absorbance at 260 nm was read for each collected fraction, and the mRNA containing fractions were pooled and ethanol precipitated at ⁇ 20° C. for 12 hours.
  • the poly(A) + RNA was collected by centrifugation, resuspended in DEPC-treated water, and stored in 5-10 ⁇ g aliquots at ⁇ 80° C.
  • Double-stranded Eco RI-Not I-directional cDNA was synthesized from 5 ⁇ g of Trichoderma reesei RutC30 poly(A) + RNA by the RNase H method (Gubler and Hoffman 1983 , Gene 25: 263-270; Sambrook et al., 1989, Molecular Cloning, a Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.) using a hair-pin modification.
  • the poly(A) + RNA (5 ⁇ g in 5 ⁇ l of DEPC-treated water) was heated at 70° C.
  • First-strand cDNA was synthesized by incubating the reaction mixture at 45° C. for 1 hour. After synthesis, the mRNA:cDNA hybrid mixture was gel filtrated through a MicroSpin S400 HR spin column (Amersham Biosciences, Piscataway, N.J.) according to the manufacturer's instructions.
  • Second strand cDNA synthesis was performed by incubating the reaction tube at 16° C. for 2 hours, and an additional 15 minutes at 25° C. The reaction was stopped by addition of EDTA to 20 mM final concentration followed by phenol and chloroform extractions.
  • the double-stranded cDNA was ethanol precipitated at ⁇ 20° C. for 12 hours by addition of 2 volumes of 96% ethanol and 0.2 volume of 10 M ammonium acetate, recovered by centrifugation, washed in 70% ethanol, dried (SpeedVac), and resuspended in 30 ⁇ l of Mung bean nuclease buffer (30 mM sodium acetate pH 4.6, 300 mM NaCl, 1 mM ZnSO 4 , 0.35 mM dithiothreitol, 2% glycerol) containing 25 units of Mung bean nuclease.
  • Mung bean nuclease buffer (30 mM sodium acetate pH 4.6, 300 mM NaCl, 1 mM ZnSO 4 , 0.35 mM dithiothreitol, 2% glycerol
  • the double-stranded cDNAs were recovered by centrifugation (30,000 ⁇ g for 30 minutes), and blunt-ended with T4 DNA polymerase in 30 ⁇ l of T4 DNA polymerase buffer (20 mM Tris-acetate, pH 7.9, 10 mM magnesium acetate, 50 mM potassium acetate, 1 mM dithiothreitol) containing 0.5 mM of each dNTP, and 5 units of T4 DNA polymerase by incubating the reaction mixture at 16° C. for 1 hour. The reaction was stopped by addition of EDTA to 20 mM final concentration, followed by phenol and chloroform extractions and ethanol precipitation for 12 hours at ⁇ 20° C. by adding 2 volumes of 96% ethanol and 0.1 volume of 3 M sodium acetate pH 5.2.
  • T4 DNA polymerase buffer 20 mM Tris-acetate, pH 7.9, 10 mM magnesium acetate, 50 mM potassium acetate, 1 mM dithiothreitol
  • cDNA was recovered by centrifugation as above, washed in 70% ethanol, and the DNA pellet was dried in a SpeedVac.
  • the cDNA pellet was resuspended in 25 ⁇ l of ligation buffer (30 mM Tris-Cl, pH 7.8, 10 mM MgCl 2 , 10 mM dithiothreitol, 0.5 mM ATP) containing 2 ⁇ g Eco RI adaptors (0.2 ⁇ g/ ⁇ l, Amersham Biosciences, Piscataway, N.J.) and 20 units of T4 ligase (Roche Molecular Biochemicals, Indianapolis, Ind.) by incubating the reaction mix at 16° C. for 12 hours.
  • the reaction was stopped by heating at 65° C. for 20 minutes, and then placed on ice for 5 minutes.
  • the adapted cDNA was digested with Not I by addition of 20 ⁇ l autoclaved water, 5 ⁇ l of 10 ⁇ Not I restriction enzyme buffer, and 50 units of Not I, followed by incubation for 3 hours at 37° C. The reaction was stopped by heating the sample at 65° C. for 15 minutes.
  • the cDNAs were size-fractionated by agarose gel electrophoresis on a 0.8% SeaPlaque GTG low melting temperature agarose gel (FMC, Rockland, Me.) in 44 mM Tris Base, 44 mM boric acid, 0.5 mM EDTA (TBE) buffer (in autoclaved water) to separate unligated adaptors and small cDNAs.
  • the gel was run for 12 hours at 15 V, and the cDNA was size-selected with a cut-off at 0.7 kb by cutting out the lower part of the agarose gel.
  • a 1.5% agarose gel was poured in front of the cDNA-containing gel, and the double-stranded cDNAs were concentrated by running the gel backwards until it appeared as a compressed band on the gel.
  • the cDNA-containing gel piece was cut out from the gel and the cDNA was extracted from the gel using a GFX Gel Band Purification Kit (Amersham, Arlington Heights, Ill.) as follows.
  • the trimmed gel slice was weighed in a 2 ml nuclease-free microcentrifuge tube (ISC BioExpress, Kaysville, Utah) then 10 ml of Capture Buffer (Amersham, Arlington Heights, Ill.) was added for each 10 mg of gel slice, the gel slice was dissolved by incubation at 60° C. for 10 minutes, until the agarose was completely solubilized, and the sample was then pelleted by a brief centrifugation (2 minutes at 8,000 ⁇ g). The melted sample was transferred to a GFX spin column placed in a collection tube, incubated at 25° C. for 1 minute, and then centrifuged at full speed (15,000 ⁇ g) in a microcentrifuge for 30 seconds.
  • a plasmid DNA preparation for a Eco RI-Not I insert-containing pYES2.0 cDNA clone was purified using a QIAGEN Tip-100 according to the manufacturer's instructions (QIAGEN, Valencia, Calif.).
  • a total of 10 ⁇ g of purified plasmid DNA was digested to completion with Not I and Eco RI in a total volume of 60 ⁇ l by addition of 6 ⁇ l of 10 ⁇ NEBuffer for Eco RI (New England Biolabs, Beverly, Mass.), 40 units of Not I, and 20 units of Eco RI followed by incubation for 6 hours at 37° C. The reaction was stopped by heating the sample at 65° C. for 20 minutes.
  • the digested plasmid DNA was extracted once with phenol-chloroform, then with chloroform, followed by ethanol precipitation for 12 hours at ⁇ 20° C. by adding 2 volumes of 96% ethanol and 0.1 volume of 3 M sodium acetate pH 5.2.
  • the precipitated DNA was resuspended in 25 ⁇ l of TE pH 7.5, loaded onto a 0.8% SeaKem agarose gel in TBE buffer, and run for 3 hours at 60 V.
  • the digested vector was cut out from the gel, and the DNA was extracted from the gel using a GFX Gel Band Purification Kit according to the manufacturer's instructions. After measuring the DNA concentration by absorbance at 260 nm, the eluted vector was stored at ⁇ 20° C. until library construction.
  • ligation buffer (30 mM Tris-Cl pH 7.8, 10 mM MgCl 2 , 10 mM DTT, 0.5 mM ATP) containing 7 ⁇ l of double-stranded cDNA (corresponding to approximately 1/10 of the total volume in the cDNA sample), 2 units of T4 ligase, and 25 ng, 50 ng and 75 ng of Eco RI-Not I cleaved pYES2.0 vector, respectively (Invitrogen, Carlsbad, Calif.).
  • the vector background control ligation reaction contained 75 ng of Eco RI-Not I cleaved pYES.0 vector without cDNA.
  • the ligation reactions were performed by incubation at 16° C. for 12 hours, heated at 65° C. for 20 minutes, and then 10 ⁇ l of autoclaved water was added to each tube.
  • One ⁇ l of the ligation mixtures was electroporated (200 W, 2.5 kV, 25 mF) to 40 ⁇ l of electrocompetent E. coli DH10B cells (Life Technologies, Gaithersburg, Md.). After addition of 1 ml of SOC medium (Birren et al., 1998 . Genome Analysis, Vol. 2 . Detecting Genes .
  • the cDNA library was stored as (1) individual pools (25,000 c.f.u./pool) in 20% glycerol at ⁇ 80° C.; (2) cell pellets of the same pools at ⁇ 20° C.; (3) QIAGEN Tip 100 purified plasmid DNA from individual pools at ⁇ 20° C.; and (4) directional, double-stranded cDNA at ⁇ 20° C.
  • Plasmid DNAs from individual E. coli colonies from the cDNA libraries described in Example 2 were purified using a 96-well manifold plasmid preparation system (QIAGEN, Valencia, Calif.) according to instructions supplied by the manufacturer.
  • CIP calf intestinal phosphatase
  • the DNA was purified again after CIP treatment and ligated with a pCR4BIunt-TOPO (Invitrogen, Carlsbad, Calif.) vector at molar ratios of 5:1 and 10:1.
  • This cloning reaction was used to transform electrocompetent E. coli TOP10 cells (Invitrogen, Carlsbad, Calif.) and 10 ⁇ l of each transformation mix was plated on LB plates containing 100 ⁇ g of ampicillin per ml and 250 ⁇ g of X-Gal per ml for blue/white screening of recombinants.
  • the transformation efficiencies using 5:1 and 10:1 molar ratios of insert-to-vector were 2.1 ⁇ 10 6 and 1.8 ⁇ 10 6 cfu/ ⁇ g, respectively.
  • a Qpix robot (Genetix Ltd., Hampshire, UK) was then used to pick the white and light blue colonies into the 96-well plates containing LB medium supplemented with 100 ⁇ g of ampicillin per ml. After overnight incubation at 37° C. an equivalent amount of 50% glycerol was added to each well, and the plates were taped with “Petri Seal” and stored at ⁇ 80° C. for later use. In total, approximately 2 ⁇ 10 5 colonies were obtained with a colony density of 300-700 per 150 mm plate. Approximately 45,000 colonies were picked, grown overnight in selective medium, and frozen in microtiter plates. This number is sufficient to give about 3 ⁇ coverage of the genome of Trichoderma reesei (ca. 94% probability of cloning every gene in the genome at least once).
  • the conditions of rolling circle amplification were optimized for the purpose of DNA microarray production to minimize the volume of starting cell material added to the TempliPhi reaction, as the RCA method is very sensitive to inhibitors from components of saturated culture medium. Moreover, excess of cell material in the reaction results in higher background of cell debris and chromosomal DNA, which might adversely impact signal-to-noise ratios during microarray experiments.
  • RNA extraction buffer was prepared by adding a freshly prepared solution of p-aminosalicylic acid (9.6 g in 80 ml of DEPC-treated water) to a solution of triisopropylnaphthalene sulfonic acid (1.6 g in 80 ml of DEPC-treated water). This mixture was added to 40 ml of 5 ⁇ RNB solution (1 M tris-HCl, pH 8.5, 1.25 M NaCl, 0.25 M EGTA) with stirring.
  • SSH suppression subtractive hybridization
  • the resulting cDNA pools from the SSH reactions in Table 1 were used to generate subtractive libraries of cellulose- and PCS-induced sequences.
  • For synthesis of cDNA 400 ng of polyA + mRNA derived from each time point (1-5 days) was combined for a total of 2 ⁇ g of template. Synthesis and subtraction of cDNA was done using a PCR-SelectTM Kit (Clontech, Palo Alto, Calif.). The methods are based on the procedure of suppression subtractive hybridization (SSH) as outlined by Diatchenko et al., 1996, supra. The overall scheme is shown in FIG. 1 .
  • mRNA was converted from three separate fermentations of Trichoderma reesei RutC30 grown on glucose, cellulose, and PCS into double-stranded cDNA using reagents supplied with the PCR-SelectTM Kit (Clontech, Palo Alto, Calif.).
  • the differentially expressed cDNAs were present in both the “tester” cDNA pool (i.e., from cells grown on cellulose or corn stover) and the “driver” cDNA, but were present at much lower levels in the “driver” pool (Table 1). Both of these cDNA pools were digested with the restriction enzyme Rsa I which recognizes a four-base pair palindrome and yields blunt-end fragments (GT
  • the tester cDNA pool was then divided into two samples and ligated with two different adaptor oligonucleotides (provided with the Clontech PCR-SelectTM Kit) resulting in two populations of tester cDNA.
  • the adaptors were designed without 5′-phosphate groups such that only the longer strand of each adaptor could be covalently linked to the 5′-ends of the cDNA.
  • type a molecules were significantly enriched for differentially expressed (e.g., cellulose- or PCS-induced) sequences, since common non-target cDNAs formed type c molecules with the driver.
  • differentially expressed e.g., cellulose- or PCS-induced
  • the two pools of primary hybridized products were combined so that the type a molecules from each tester sample could associate and form new type e hybrids. These were double-stranded tester molecules with different adaptor sequences on each end. Fresh denatured driver cDNA was also added to further enrich the pool of e molecules for differentially expressed sequences.
  • the differentially expressed cDNAs were selectively amplified by PCR (conditions specified in the PCR-SelectTM Kit) Only type e molecules that have two different primer annealing sites were amplified exponentially.
  • the cDNA clones from approximately 360 randomly picked colonies were purified by rolling circle amplification using an Amersham TempliPhi Kit and analyzed by DNA sequencing (70 from Reaction 1, 96 from Reaction 2, and 192 from Reaction 3). Clustering of the sequences using Transcript AssemblerTM software (Paracel, Inc., Pasadena, Calif.) showed that each pool contained a high percentage of non-redundant clones—76% for Reaction 1, 90% for Reaction 2, and 67% for Reaction 3. In addition, the contigs (overlapping sequences of the same cDNA) identified in this analysis contained on average only two sequences.
  • Subtracted and normalized cDNA fractions generated by the SSH procedure were ligated with pCR11-TOPO (Invitrogen, Carlsbad, Calif.) and the ligation mixtures were used to transform electrocompetent E. coli TOP10 cells (Invitrogen, Carlsbad, Calif.). Transformants were selected on LB agar plates (Miller, J. H. 1992. A short course in bacterial genetics. A laboratory manual and handbook for Escherichia coli and related bacteria. Cold Spring Harbor Press, Cold Spring Harbor, N.Y.) that contained 250 ⁇ g/ml X-Gal (no IPTG) and ampicillin at a final concentration of 100 ⁇ g/ml.
  • the cDNA clones from approximately 360 randomly picked colonies were purified by rolling circle amplification (RCA) (Dean et al., 2001 , Genome Res. 11: 1095-1099) and analyzed by DNA sequencing (70 from Reaction 1, 96 from Reaction 2, and 192 from Reaction 3). Clustering of the sequences using Transcript AssemblerTM software showed that each pool contained a high percentage of non-redundant clones: 76% for reaction 1, 90% for reaction 2, and 67% for reaction 3. In addition, the contigs (overlapping sequences of the same cDNA) identified in this analysis contained on the average only two sequences. Collectively, these observations suggested that efficient normalization of the libraries was achieved during the SSH reactions, yielding a low level of redundancy in the corresponding cDNA libraries.
  • RCA rolling circle amplification
  • Plasmid DNA samples from 3608 colonies representing the three SSH cDNA libraries (1152 clones each from SG and SC libraries, and 1304 clones from the CG library) were prepared using rolling-circle amplification (RCA).
  • RCA (Dean et al., 2001, supra) of plasmid DNA from frozen cells was done using TempiPhiTM reagents (Amersham, Arlington Heights, Ill.).
  • the amplified cDNA clones were diluted to a concentration of 100-400 ng/ ⁇ l in 3 ⁇ SSC and spotted from 384-well plates onto poly-L-lysine coated glass microscope slides using equipment and methods that were described previously (Eisen and Brown, 1999 , Methods Enzymol. 303: 179-205).
  • Several control DNAs were included as well: cbh1, cbh2, egl1, egl2, serine hydroxymethyl transferase cDNA, ⁇ -actin, and 28S rDNA.
  • Fluorescent probes were prepared by reverse transcription of poly(A) + RNA, incorporating aminoallyl-dUTP into first strand cDNA (Berka et al., 2003 , Proc. Nat Acad. Sci. USA 100: 5682-5687). The amino-cDNA products were subsequently labeled by direct coupling to either Cy3 or Cy5 monofunctional reactive dyes (Amersham, Arlington Heights, Ill.) and purified as described previously (Berka et al., 2003, supra). In all cases, cDNA from cells grown on glucose was used as the control (Cy3 label), and cDNA from cells grown on cellulose or PCS was labeled with Cy5.
  • Cy3 and Cy5 labeled probes were combined, purified using a QIAquick PCR Purification Kit (QIAGEN, Valencia, Calif.) and dried under vacuum, resuspended in 15.5 ⁇ l of water, and combined with the following: 3.6 ⁇ l of 20 ⁇ SSC, 2.5 ⁇ l of 250 mM HEPES (pH 7.0), 1.8 ⁇ l of poly-dA (500 ⁇ g/ml), and 0.54 ⁇ l of 10% SDS. Before hybridization, the solution was filtered with a 0.22 ⁇ m filter, heated to 95° C. for 2 minutes, and cooled to room temperature.
  • the fluorescently labeled cDNAs were applied to microarrays under cover glasses, placed in a humidified chamber, and incubated at 63° C. overnight (15-16 hours). Before scanning, the arrays were washed consecutively in 1 ⁇ SSC with 0.03% SDS, 0.2 ⁇ SSC, and 0.05 ⁇ SSC and centrifuged for 2 minutes at 500 rpm to remove excess liquid. Microarray slides were imaged using an Axon GenePix® 4000B Scanner (Axon Instruments, Union City, Calif.), and the fluorescence signals for microarray spots were quantified using GenePix® Pro 5.0 software (Axon Instruments). PMT voltages were adjusted during image collection such that the average ratio of fluorescence intensities for the entire array was approximately 1.0.
  • the S+ ArrayAnalyzer 2.0 microarray analysis software (Insightful Corporation, Seattle, Wash.) was used for analyzing of the microarray data.
  • Raw fluorescence intensity values were normalized using the loess function and differential expression analysis was performed using the LPE test. Those spots that were statistically significant (P ⁇ 0.1) in the LPE test and for which change in the Cy5:Cy3 intensity ratios were greater than 2.0 were chosen for DNA sequencing analysis.
  • SEQ ID NOs. 1-1188 The sequences of the Trichoderma reesei ESTs and SSH dones are designated SEQ ID NOs. 1-1188.
  • An “N” in a nucleic acid sequence means that the nucleotide is an A, C, G, or T.
  • SEQ ID NOs: 1-24 are the ESTs and SEQ ID NOs: 25-1188 are the SSH clones.
  • the ESTs and SSH clones were compared by means of computer algorithms for homologies to the content of individual families. All sequences from a given family were used individually as a query to search a database of EST sequences of the invention using a number of different homology search algorithms like FASTA and BLAST (W. R. Pearson, 1990. Rapid and Sensitive Sequence Comparison with FASTP and FASTA, Methods in Enzymology 183: 63-98; and Altschul, Stephen F., Warren Gish, Webb Miller, Eugene W. Myers, and David J. Lipman, 1990, Basic local alignment search tool, Journal of Molecular Biology 15: 403-10).
  • a distinct hit to a sequence of a given family predicted the particular EST or SSH clone sequence to encode a protein of that family.
  • part of the EST and SSH clone sequences listed in Table 4 were shown to belong to distinct enzyme families.

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